The present invention provides stem cells loaded with bi-functional magnetic nanoparticles (nanoparticle-loaded stem cells (NLSC)) that both: a) heat in an alternating magnetic field (AMF); and b) provide MRI contrast enhancement for MR-guided hyperthermia. The nanoparticles in the NLSC are non-toxic, and do not alter stem cell proliferation and differentiation, the nanoparticles do however, become heated in an alternating magnetic field, enabling therapeutic applications for cancer treatment. Due to the fact that circulating stem cells home to tumors and metastasis, and participate in neovascularization of growing tumors, the NLSC of the present invention allows tracking of the tissue distribution of infused stem cells and selective heating of targeted tissues with AMF. NLSC can deliver hyperthermia to hypoxic areas in tumors for sensitization of those areas to subsequent treatment, thus delivering therapy to the most treatment-resistant tumor regions. The heating of diseased tissue either results in direct cell killing or makes the tumor more susceptible to radio- and/or chemotherapy. The targeted hyperthermia provided by the present invention has clinical potential because it is associated with fewer side effects, and can also be used in combination with conventional treatment modalities, significantly enhancing their effectiveness. The NLSC of the present invention can be used for MR image-guided hyperthermia in oncology, in stem cell research for cell tracking and heating, and for elimination of mis-injected stem cells.